Pests of jatropha_Bionomics_identification_Dr.UPR.pdf
Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas
1. Cis-regulatory somatic mutations and
gene-expression alteration in B-cell lymphomas
A. Mathelier, C. Lefebvre, A.W. Zhang, D.J. Arenilas, J. Ding,
W.W. Wasserman, and S.P. Shah
Genome Biology, 2015, 16:84
2015 June 8th
anthony.mathelier@gmail.com @AMathelier
1
2. A cancer gene discovery gap
M.S. Lawrence et al.,
Nature, 2013.
Highly mutated cancer genes revealed through The Cancer
Genome Atlas project.
Still a discovery gap in the search of new cancer genes.
We assert this gap can be partially filled through the analysis
of the non-coding genome.
2
3. Cis-regulatory mutations may impact gene expression
Variation
TF
..GATCC.. ..GAACC..
TF
TFBS
adapted from W. Shi’s figure
3
4. Cis-regulatory mutations may impact gene expression
Variation
TF
..GATCC.. ..GAACC..
TF
TFBS
adapted from W. Shi’s figure
One needs to accurately locate TFBSs to identify and characterize
the regulatory sequences controlling specific genes transcription.
3
5. Predicting cis-regulatory elements genome wide
...gctaaGTAACAATgcgca...
...cttaaGTAAACATcgctc...
...ccaatGTAAACAAacgga...
MANTA
Adapted from Szalkowski and Schmid.
Briefings in Bioinfomatics, 2010
Mathelier et al.,
Nucleic Acids Research, 2014.
4
6. TFBSs defined as cis-regulatory elements
477 ChIP-seq data from ENCODE and literature
103 TFs with a JASPAR2014 TF binding profiles
76,160,599bp in TFBSs predicted in ChIP-seq peaks
(∼2% of the human genome)
5
7. Somatic cis-regulatory mutations in B-cell lymphomas
Whole genome sequence for 84 B-cell lymphoma patient
samples with matched control samples :
cohort 1 : 40 diffuse large B-cell lymphomas (DLBCL)
cohort 2 : 44 of mixed histology – 14 Burkitt lymphomas, 15
DLBCLs, 1 primary mediastinal B-cell lymphoma (PMBCL),
and 14 follicular lymphomas (FL)
406,611 SNVs and 15,739 indels in samples from cohort 1
282,636 SNVs and 8,080 indels in samples from cohort 2
RNA-seq for the cancer samples
Richter et al., Nat. Genetics, 2012 ; Morin et al., Blood, 2013
6
9. Promoters are frequent targets of cis-regulatory mutations
A BCohort1 Cohort2
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
x
y
HIST1H1B
ST6GAL1
TMSB4X
ZFP36L1
NEDD9
BCL7A
RHOH
BIRC3
CIITA
IG
LL5
BTG2
SG
K1
CD74
BCL2
BCL6
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
x
y
HIST1H1C
HIST1H1E
TMSB4X
ZFP36L1
BCL2L11
BZRAP1
DNM
T1
ZNF860
N
CO
A3
FOXO1
BACH2
CXCR4
DUSP2
RFTN1
TCL1A
BCL7A
SOCS1
SEPT9
P2RX5
S1PR2
RHOH
EPS15
BIRC3
CIITA
DTX1
IG
LL5
BTG2
BTG1 SG
K1
CD74
CD83
BCL2
BCL6
PIM1
MYC
B2M
IRF1
IRF4
LTB
ID3
p = 1.16 x 10-75
p = 3.28 x 10-156
12 genes targeted in both cohorts independently
Additional 13 genes from combined cohorts not previously
described as hypermutated
−→ 6 of them exclusively mutated in their promoters 7
10. Promoters of apoptic, B-cell, and cancer pathway genes
are frequent targets of cis-regulatory mutations
Cohort1
lymphoma
small cell lung
cancer
apoptosis
in apoptotic
signaling
role of
mitochondria
hiv-1 nef:
negative
effector of fas
and tnf
keratinocyte
differentiation
ceramide
signaling
pathway
regulation of B
cell
proliferation
positive
regulation of B
cell
proliferation
lymphocyte
differentiationnegative
regulation of
lymphocyte
apoptotic
process
leukocyte
activation
negative
regulation of B
cell apoptotic
process
regulation of B
cell activation
leukocyte
differentiation
positive
regulation of
lymphocyte
proliferation
regulation of
cell growth
lymphocyte
activation
T cell
differentiation
positive
regulation of B
cell activation
negative
regulation of
intracellular
signal
transduction
positive
regulation of
leukocyte
proliferation
regulation of
type 2 immune
response
regulation of B
cell apoptotic
process
negative
regulation of T
cell
differentiation
positive
regulation of
mononuclear
cell
proliferation
GO Biological
Process OMIM
KEGG
Pathway BioCarta
FDR < 0.05
8
11. Landscape of mutations and altered gene expression
mutation
TFBS
Protein-coding exon
TSS
A
B
C
xseq input
Ding et al., submitted.
9
13. Predicted genes and their deregulated interactors are
enriched for pathways related to cancer
Cohort2
phosphatidylinositol
signaling
system
chronic
myeloid
leukemia
gliomahuntingtons
disease
focal adhesion pancreatic
cancer
small cell lung
cancer
endometrial
cancer
non small cell
lung cancer
colorectal
cancer
cell cycle
prostate cancer
calcium
signaling
pathway
inositol
phosphate
metabolism
erbb signaling
pathway
mapk signaling
pathway
vegf signaling
pathway
long term
potentiation
fc epsilon ri
signaling
pathway
gnrh signaling
pathway
Cohort1
chronic
myeloid
leukemia
erbb signaling
pathway
acute myeloid
leukemia
pancreatic
cancer
prostate cancer
endometrial
cancer
glioma
ecm receptor
interaction
focal adhesion
epithelial cell
signaling in
helicobacter
pylori infection
renal cell
carcinoma
small cell lung
cancer
oxidative
phosphorylation
colorectal
cancer
WikiPathways
FDR < 0.05
10
15. Summary
We analyzed ∼ 700, 000 somatic mutations from 84 B-cell
lymphoma samples
We characterized a set of cis-regulatory elements from
ChIP-seq
Cis-regulatory mutations are enriched in promoter regions of
genes involved in apoptosis or growth/proliferation
We combined gene expression and mutation data from the
coding and non-coding spaces
We highlight candidate regulatory-disrupting variations
dysregulating the gene expression program in cancer pathways
12
16. Acknowledgements
Wasserman lab :
Wyeth Wasserman
David Arenillas
Allen Zhang
all the Wasserman lab members
Shah lab :
Sohrab Shah
Calvin Lefebvre
Jiarui Ding
Funding :
Centre for Molecular Medicine
and Therapeutics
13